DeepTrack2 is a modular Python library for generating, manipulating, and analyzing image data pipelines for machine learning and experimental imaging.
The Open Free Energy toolkit
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.
APBS - software for biomolecular electrostatics and solvation
Software for biomolecular electrostatics and solvation calculations
Differentiable neuron simulations with biophysical detail on CPU, GPU, or TPU.
A Python platform for Structural Bioinformatics
Analysis of non-covalent interactions in MD trajectories
Python library for diffraction tomography with the Born and Rytov approximations
Modeling molecular ensembles with scalable data structures and parallel computing
a package to simulate fluid surfaces and biomembranes
APBS & PDB2PQR - software for biomolecular electrostatics and solvation
Pras Server is a library to repair PDB or mmCIF structures, add missing heavy atoms and hydrogen atoms and assign secondary structure by amide-amide interactions of the backbone
KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.
Oil Palm Growth and Yield Model
A python library for advanced lattice light-sheet image analysis
EP-PINNs implementation for 1D and 2D forward and inverse solvers for the Aliev-Panfilov cardiac electrophysiology model. Also includes Matlab finite-differences solver for data generation.
Robust and stable clustering of molecular dynamics simulation trajectories.
a Living ENsemble Simulator -- a lens to help you watch biophysics
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